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  <h1>Source code for pymatgen.symmetry.structure</h1><div class="highlight"><pre>
<span></span><span class="c1"># coding: utf-8</span>
<span class="c1"># Copyright (c) Pymatgen Development Team.</span>
<span class="c1"># Distributed under the terms of the MIT License.</span>

<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">This module implements symmetry-related structure forms.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">List</span>

<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>

<span class="kn">from</span> <span class="nn">tabulate</span> <span class="kn">import</span> <span class="n">tabulate</span>

<span class="kn">from</span> <span class="nn">pymatgen.core.structure</span> <span class="kn">import</span> <span class="n">Structure</span><span class="p">,</span> <span class="n">PeriodicSite</span>


<div class="viewcode-block" id="SymmetrizedStructure"><a class="viewcode-back" href="../../../pymatgen.symmetry.structure.html#pymatgen.symmetry.structure.SymmetrizedStructure">[docs]</a><span class="k">class</span> <span class="nc">SymmetrizedStructure</span><span class="p">(</span><span class="n">Structure</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    This class represents a symmetrized structure, i.e. a structure</span>
<span class="sd">    where the spacegroup and symmetry operations are defined. This class is</span>
<span class="sd">    typically not called but instead is typically obtained by calling</span>
<span class="sd">    pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_symmetrized_structure.</span>

<span class="sd">    .. attribute: equivalent_indices</span>

<span class="sd">        indices of structure grouped by equivalency</span>
<span class="sd">    &quot;&quot;&quot;</span>

    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure</span><span class="p">:</span> <span class="n">Structure</span><span class="p">,</span>
                 <span class="n">spacegroup</span><span class="p">,</span>
                 <span class="n">equivalent_positions</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span>
                 <span class="n">wyckoff_letters</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">str</span><span class="p">]):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Args:</span>
<span class="sd">            structure (Structure): Original structure</span>
<span class="sd">            spacegroup (SpacegroupOperations): An input SpacegroupOperations from</span>
<span class="sd">                SpacegroupAnalyzer.</span>
<span class="sd">            equivalent_positions: Equivalent positions from SpacegroupAnalyzer.</span>
<span class="sd">            wyckoff_letters: Wyckoff letters</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">spacegroup</span> <span class="o">=</span> <span class="n">spacegroup</span>
        <span class="n">u</span><span class="p">,</span> <span class="n">inv</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">equivalent_positions</span><span class="p">,</span> <span class="n">return_inverse</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">site_labels</span> <span class="o">=</span> <span class="n">equivalent_positions</span>

        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
            <span class="n">structure</span><span class="o">.</span><span class="n">lattice</span><span class="p">,</span> <span class="p">[</span><span class="n">site</span><span class="o">.</span><span class="n">species</span> <span class="k">for</span> <span class="n">site</span> <span class="ow">in</span> <span class="n">structure</span><span class="p">],</span>
            <span class="n">structure</span><span class="o">.</span><span class="n">frac_coords</span><span class="p">,</span> <span class="n">site_properties</span><span class="o">=</span><span class="n">structure</span><span class="o">.</span><span class="n">site_properties</span><span class="p">)</span>

        <span class="n">equivalent_indices</span> <span class="o">=</span> <span class="p">[[]</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">u</span><span class="p">))]</span>  <span class="c1"># type: ignore</span>
        <span class="n">equivalent_sites</span> <span class="o">=</span> <span class="p">[[]</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">u</span><span class="p">))]</span>  <span class="c1"># type: ignore</span>
        <span class="n">wyckoff_symbols</span> <span class="o">=</span> <span class="p">[[]</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">u</span><span class="p">))]</span>  <span class="c1"># type: ignore</span>
        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">inv</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">inv</span><span class="p">):</span>
            <span class="n">equivalent_indices</span><span class="p">[</span><span class="n">inv</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
            <span class="n">equivalent_sites</span><span class="p">[</span><span class="n">inv</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sites</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
            <span class="n">wyckoff_symbols</span><span class="p">[</span><span class="n">inv</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">wyckoff_letters</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_indices</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="n">equivalent_indices</span>  <span class="c1"># type: ignore</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_sites</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">PeriodicSite</span><span class="p">]</span> <span class="o">=</span> <span class="n">equivalent_sites</span>  <span class="c1"># type: ignore</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">wyckoff_letters</span> <span class="o">=</span> <span class="n">wyckoff_letters</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">wyckoff_symbols</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;</span><span class="si">%d%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">w</span><span class="p">),</span> <span class="n">w</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
                                <span class="k">for</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">wyckoff_symbols</span><span class="p">]</span>

<div class="viewcode-block" id="SymmetrizedStructure.copy"><a class="viewcode-back" href="../../../pymatgen.symmetry.structure.html#pymatgen.symmetry.structure.SymmetrizedStructure.copy">[docs]</a>    <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        :return: Copy of structure.</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">spacegroup</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">spacegroup</span><span class="p">,</span>
                              <span class="n">equivalent_positions</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">site_labels</span><span class="p">,</span>
                              <span class="n">wyckoff_letters</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">wyckoff_letters</span><span class="p">)</span></div>

<div class="viewcode-block" id="SymmetrizedStructure.find_equivalent_sites"><a class="viewcode-back" href="../../../pymatgen.symmetry.structure.html#pymatgen.symmetry.structure.SymmetrizedStructure.find_equivalent_sites">[docs]</a>    <span class="k">def</span> <span class="nf">find_equivalent_sites</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">site</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="n">PeriodicSite</span><span class="p">]:</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Finds all symmetrically equivalent sites for a particular site</span>

<span class="sd">        Args:</span>
<span class="sd">            site (PeriodicSite): A site in the structure</span>

<span class="sd">        Returns:</span>
<span class="sd">            ([PeriodicSite]): List of all symmetrically equivalent sites.</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="k">for</span> <span class="n">sites</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">equivalent_sites</span><span class="p">:</span>
            <span class="k">if</span> <span class="n">site</span> <span class="ow">in</span> <span class="n">sites</span><span class="p">:</span>
                <span class="k">return</span> <span class="n">sites</span>

        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Site not in structure&quot;</span><span class="p">)</span></div>

    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>

    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="n">outs</span> <span class="o">=</span> <span class="p">[</span>
            <span class="s2">&quot;SymmetrizedStructure&quot;</span><span class="p">,</span>
            <span class="s2">&quot;Full Formula (</span><span class="si">{s}</span><span class="s2">)&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">s</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">composition</span><span class="o">.</span><span class="n">formula</span><span class="p">),</span>
            <span class="s2">&quot;Reduced Formula: </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">composition</span><span class="o">.</span><span class="n">reduced_formula</span><span class="p">)]</span>

        <span class="k">def</span> <span class="nf">to_s</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
            <span class="k">return</span> <span class="s2">&quot;</span><span class="si">%0.6f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">x</span>
        <span class="n">outs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;abc   : &quot;</span> <span class="o">+</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">to_s</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">.</span><span class="n">rjust</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
                                           <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">abc</span><span class="p">]))</span>
        <span class="n">outs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;angles: &quot;</span> <span class="o">+</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">to_s</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">.</span><span class="n">rjust</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
                                           <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">angles</span><span class="p">]))</span>
        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_charge</span><span class="p">:</span>
            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_charge</span> <span class="o">&gt;=</span> <span class="mi">0</span><span class="p">:</span>
                <span class="n">outs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;Overall Charge: +</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_charge</span><span class="p">))</span>
            <span class="k">else</span><span class="p">:</span>
                <span class="n">outs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;Overall Charge: -</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_charge</span><span class="p">))</span>
        <span class="n">outs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;Sites (</span><span class="si">{i}</span><span class="s2">)&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)))</span>
        <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="n">props</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">site_properties</span>
        <span class="n">keys</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">props</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">sites</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">equivalent_sites</span><span class="p">):</span>
            <span class="n">site</span> <span class="o">=</span> <span class="n">sites</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
            <span class="n">row</span> <span class="o">=</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">),</span> <span class="n">site</span><span class="o">.</span><span class="n">species_string</span><span class="p">]</span>
            <span class="n">row</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">to_s</span><span class="p">(</span><span class="n">j</span><span class="p">)</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">site</span><span class="o">.</span><span class="n">frac_coords</span><span class="p">])</span>
            <span class="n">row</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">wyckoff_symbols</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
            <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">:</span>
                <span class="n">row</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">props</span><span class="p">[</span><span class="n">k</span><span class="p">][</span><span class="n">i</span><span class="p">])</span>
            <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
        <span class="n">outs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tabulate</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;#&quot;</span><span class="p">,</span> <span class="s2">&quot;SP&quot;</span><span class="p">,</span> <span class="s2">&quot;a&quot;</span><span class="p">,</span> <span class="s2">&quot;b&quot;</span><span class="p">,</span> <span class="s2">&quot;c&quot;</span><span class="p">,</span> <span class="s2">&quot;Wyckoff&quot;</span><span class="p">]</span> <span class="o">+</span> <span class="n">keys</span><span class="p">,</span>
                             <span class="p">))</span>
        <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">outs</span><span class="p">)</span>

<div class="viewcode-block" id="SymmetrizedStructure.as_dict"><a class="viewcode-back" href="../../../pymatgen.symmetry.structure.html#pymatgen.symmetry.structure.SymmetrizedStructure.as_dict">[docs]</a>    <span class="k">def</span> <span class="nf">as_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        :return: MSONAble dict</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="k">return</span> <span class="p">{</span>
            <span class="s2">&quot;structure&quot;</span><span class="p">:</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">as_dict</span><span class="p">(),</span>
            <span class="s2">&quot;spacegroup&quot;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">spacegroup</span><span class="p">,</span>
            <span class="s2">&quot;equivalent_positions&quot;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">site_labels</span><span class="p">,</span>
            <span class="s2">&quot;wyckoff_letters&quot;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">wyckoff_letters</span>
        <span class="p">}</span></div>

<div class="viewcode-block" id="SymmetrizedStructure.from_dict"><a class="viewcode-back" href="../../../pymatgen.symmetry.structure.html#pymatgen.symmetry.structure.SymmetrizedStructure.from_dict">[docs]</a>    <span class="nd">@classmethod</span>
    <span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">d</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        :param d: Dict representation</span>
<span class="sd">        :return: SymmetrizedStructure</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="k">return</span> <span class="n">SymmetrizedStructure</span><span class="p">(</span>
            <span class="n">Structure</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s2">&quot;structure&quot;</span><span class="p">]),</span>
            <span class="n">spacegroup</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">&quot;spacegroup&quot;</span><span class="p">],</span>
            <span class="n">equivalent_positions</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">&quot;equivalent_positions&quot;</span><span class="p">],</span>
            <span class="n">wyckoff_letters</span><span class="o">=</span><span class="n">d</span><span class="p">[</span><span class="s2">&quot;wyckoff_letters&quot;</span><span class="p">]</span>
        <span class="p">)</span></div></div>
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